A Message in Time
by heintz571
Summary: To save the Doctor from Area 51, River enlists Amy's help to save him but it may come at a cost, for the timelines are in flux all around them.
1. Chapter 1

**I do hope you enjoy this story the plot bunnies were demanding that it be written. If you have the time please read and review. with many thanks Flydye**

Title: A Message in Time

Author: Flydye8

Pairings: Eleven/Amy, River/Amy, and another companion

Rating: PG-13

Disclaimer: I don't own Doctor Who I never will (sighs in sadness)

Summary: To save the Doctor from Area 51, River enlists Amy's help to save him but it may come at a cost, for the timelines are in flux all around them.

Author's Note: I have been keeping an eye on all the possible spoilers for Season 6 of Doctor Who. I have read and listen to the possible storylines. As I read and listened a plot bunny appeared to me via my muses and has demanded I write this story. I even tried to continue on my Silence series but this bunny was relentless. So here it is, maybe once I get it out of my system I can focus writing other stuff.

The TARDIS jolted to the side, forcing the Doctor to grab onto the consol to stay afoot so he could try to stabilize the ancient craft. Emerging at the top of the stairs, a young woman with shoulder length wavy, red hair tried to move down the steps safely as the TARDIS jolted to the opposite side.

Barely gaining her footing she stumbled to the Doctors side and asked, "What the hell is happening with the TARDIS?"

"I don't know Brianne we seem to be caught in some sort of time loop caused by some outside force…I have not experienced anything like this in years, not since I traveled with..." Directing her to the zig- zag plotter he continued, "Move the plotter quickly it helped the last time, hopefully it will help this time as well."

Brianne moved toward the plotter, taking a glanced behind her she aligned herself to the TARDIS doors; then took three steps to the right and moved the handle of the plotter. Slowly the TARDIS started to stabilize, but the rotor in the center of the ship sounded a still a bit off.

Clapping his hands the Doctor congratulated, "Nice job in remembering where to stand you are learning very well my…" his statement was never finished as a bright beam enveloped the Doctor yanking him from the inside of the TARDIS.

With a yell, Brianne lunged forward in a desperate attempt to grab the Doctor; falling through the beam of light she collided with the console. Within moments the TARDIS thrashed again causing some of the delicate instruments to spark and catch fire.

Moving quickly around the center console, Brianne turned bits of knobs and switches finally ending in moving the zig-zag plotter.

As she continued to fly the TARDIS a flash of light appeared from behind her, without even looking over her shoulder Brianna stated, "It is about time you got her River, I have to land the TARDIS and I can't do it by myself yet. I need your help.

"No problem sweetie that is why I am here." Moving opposite of Brianne; they worked the controls without saying a word both knowing what they had to do to get the ancient ship to materialize safely.

Once they were landed Brianne sat on the bench seat and sighed in relief, "You know River you really should just start traveling with us instead of popping up."

Smiling at her River replied as she looked at the screen, "You know it isn't my time yet. We are on Earth year 2011. So tell me what happened that you ended up being on the TARDIS by yourself before you were ready to pilot her properly?"

"Like you don't know; why don't you look in your blue book."

"Well this time I don't know the TARDIS sent an emergency message to me. I tell you the TARDIS has lousy timing, I was close to an important find; this is going to set my work back by at least a couple of weeks."

Astonished Brianne turned to her, "So you have no idea what is going on."

"Nope sweetie I am just in the dark as you are. So tell me what happened." River encouraged.

After explaining everything Brianne asked, "So what do you think?"

"What I think is that we need to look through the data base and find out when the Doctor encountered this before and then of course we need to save him."

Standing up River typed some information into the computer and waited for the results; as the screen showed the information she shook her head, "Oh this is not good, not good at all."

Pressing a few more buttons on the screen an image of Amelia Pond appeared, "If you are watching this the Doctor has encountered another attempt to build a TARDIS and you are probably in the year 2011. Listen, Brianne and River, the Doctor is being held at Area 51 and has been captive by the forces there for about three months. You need to rescue the Doctor and destroy the TARDIS prototype you will also need to find me because you will need my help. Rory, the Doctor, and I will be in the same time as you now hurry, time is short."

As the image faded Brianne wiped the tears from her cheeks trying to settle her mixed feelings.

Seeing Brianne distress River went and hugged her, "Are you going to be alright."

Adjusting her shoulders Brianne sniffed loudly as she pulled away from the motherly embrace, "Yeah I will be alright, but I don't like this. Things could go terribly wrong. I don't like how the timelines are in flux; this could be bad very bad. What happens needs to happen; too much is at stake for it not to."

"Don't worry we will keep the timelines, in line, so to speak we will just have to be very careful."

"What if she asks me questions what am I suppose to say?" Brianne asked.

"Do what I always do sweetie, spoilers." River responded with a broad smile, before continuing, "I am going to find Amy Pond. While I am away, why don't you look up the schematics of Area 51 and find the best way to get in there and where the prototype and the Doctor may be."

"Okay, and River be careful you don't know what is out there." Brianne cautioned.

Heading out the door, River called back, "You know you are started to sound like him as well."

"Well thank you for your kind compliment." Brianne countered.

River's laugh echoed as Brianne turned toward the console, "Okay old girl will you bring up the schematics." Instantly the screen flashed, and the information requested appeared rapidly in front of her eyes. A few minutes later Brianne sat down and started to make a plan on how to get the Doctor out. Amy was right they were going to need her help.

The Doctor pressed a final button on the console and called out, "We are here Pond; Paris, France."

Hearing no reaction or snide remarks from Amy; he looked over to the bench seat, and found her fast asleep snoring. He looked at her worriedly, over the last couple of weeks he had noticed her tiring much faster than before. Which was one of the reasons they were visiting France. They all needed a good rest after their last few adventures maybe all the adventure was taking its toll on her body.

Hearing footsteps the Doctor saw Rory appear holding a cup of tea. Motioning with his fingers he led the young man away from the sleeping women.

"She is asleep again isn't she?" Rory asked with worry.

"Yes, yes she is, you need to let her get some sleep Rory we lead a very active life."

"Oh it is not me that is keeping her up, Doctor. When she goes to bed she is snoring away almost immediately."

A voice called out interrupting their conversation, "I have told you before, Rory I do not snore."

Rory and the Doctor just looked at each other knowingly; they both knew that she snored but choose not to say anything to the temperamental red head.

As Amy approached her boys she reached for the cup of tea and took a tentative sip, "What, neither of you are going to argue with me about my snoring."

"Um no." Rory replied before continuing, "So Doctor are you sure we are in Paris?"

"Of course I am sure we are in Paris, why would you question me." The Doctor replied haughtily.

Snicker Amy commented, "Because Doctor, your track record isn't very good."

Pointing his finger at her the Doctor turned on the balls of his feet and moved to the TARDIS doors, and opened them dramatically, then stepped outside, "Come out and see Paris, France."

Rory and Amy just looked at each other and rolled their eyes as the followed the Doctor outside. Seeing the desert landscape with the red rocks jotting from the ground Amy snickered, "I don't think this is Paris, Doctor."

Looking around him he noticed for the first time the surrounding landscape, he hurried back into the TARDIS as Rory and Amy laughed. After a few moments the Doctor re-emerged wearing a Stetson hat.

Rory asked as he pointed to the Doctor's head gear, "What is that?"

"It is a Stetson, I wear a Stetson now, Stetsons are cool. You should get…"

His last words were lost with resounding sound of gun fire and the Stetson falling to the ground.

As they turned around they saw River with a smoking gun, they watched as she blew the excess smoke from her weapon, "Hello sweetie."

The Doctor just smiled apprehensively, the last time they met she told him that everything would change and he didn't want anything to change he was happy with the way things were.

Amy stepped forward and gave the older woman a hug, "Thank you for helping me to remember."

"Oh it was my pleasure Hon." River smiled fondly at her.

"River?" the Doctor started as he stride forward, "Why are you here this time?"

"Oh Doctor, spoilers besides I am not here for you."

"Then who… are you here for River?" the Doctor asked suspiciously.

Smiling secretively, "I am here for Amy. I need her help with something."

"There is no way Amy is going anywhere without _me!_" The Doctor exclaimed.

"Or me." Rory chimed in.

Lifting her hand up, River blew a powdery substance on the men, "Sorry, boys I can't let you interfere."

Amy watched as her husband and the Doctor fell to the ground, moving quickly to their sides she glared at River, "I swear if you hurt them, you will be sorry!"

Kneeling down she grabbed the Doctor under his armpits and dragged him into the TARDIS. Amy made a move to do the same with her husband when River stopped her, "No, Amy don't move him it is too dangerous."

"How can moving my hubby inside be dangerous?" she knelt to start moving him again, when River dropped the Doctor unceremoniously and moved quickly to her side halting her movements.

"Trust me Amy, let me move him you should not be lifting anything."

Standing up Amy watched as River moved the two men inside the TARDIS and called out, "What are you not telling me River?"

Bringing her finger to her mouth she tapped her lips, "Spoilers, sweetie, spoilers." Closing the TARDIS doors she turned to Amy, "Now come on time is a wasting and the Doctor needs saved."

"What do you mean the Doctor needs saved, he is in the TARDIS." Amy asked.

"Not this Doctor, the Doctor from the future." River replied.

"Oh this is going to get all timey whimey again isn't it?" Amy inquired

"Hopefully not too bad, but yes it will get a bit complicated."


	2. Chapter 2

**Thank you for continuing to read if you have the time please review With thanks Flydye**

Title: A Message in Time 2/4

Author: Flydye8

Pairings: Eleven/Amy, River/Amy, and another companion

Rating: PG-13

Disclaimer: I don't own Doctor Who I never will (sighs in sadness)

Summary: To save the Doctor from Area 51, River enlists Amy's help to save him but it may come at a cost, for the timelines are in flux all around them.

Author's Note: I have been keeping an eye on all the possible spoilers for Season 6 of Doctor Who. I have read and listen to the possible storylines. As I read and listened a plot bunny appeared to me via my muses and has demanded I write this story. I even tried to continue on my Silence series but this bunny was relentless. So here it is, maybe once I get it out of my system I can focus writing other stuff.

The Doctor sat in his dark cell, his back curled up with his forehead on his knees. It has been a long three months under the close examination of the scientific staff at Area 51. He had been poked, prodded and all around violated for his knowledge on TARDIS technology. As of yet he still hadn't figured out who was actually in charge of producing the prototype, that they were trying to develop. He knew that whoever was in charge they were non-terrestrial and had fearsome technology at their disposal.

At first he thought that it might be the Daleks because the beam used to transport him out of his TARDIS was so similar to the one that invaded the walls of the ancient craft during his ninth incarnation. Thinking of his beloved ship he said a silent prayer to the universal gods, that Brianne and his ship were safe. He hoped that if something happened to either of them he would sense it through the timelines. Especially since the three of them were so intricately connected.

He took some deep breaths preparing him for some much needed restorative sleep when he felt a ripple in the timelines standing up he rushed to the small window, as he looked out at the darkness he whispered, "No, No, this is not good, not good at all. What are you doing? This is dangerous, Brianne very, very dangerous."

Pulling away from the window his hearts constricted with fear, but was soon replaced with hope. Brianne was nearby and even if he questioned what she was doing; he knew that nothing would keep her from him. He would be rescued soon, closing his eyes the Doctor fell into a deep sleep; he was going to need his strength.

Brianne paced the central control room of the TARDIS trying to calm down without success. Meeting Amelia Pond was not something she ever thought she would have to do. Of course the Doctor talked about her often and she knew that he loved her very deeply, there was no way she could question that love in her lifetime and beyond it just wasn't possible.

Hearing a tiny hum in the back of her mind, Brianne moved to the screen and watched as River and Amelia came closer to the TARDIS. Taking a deep breath she sat and waited for the duo to enter the TARDIS.

As they entered Amy clarified, "So you are saying I left a message for you guys telling you that you needed to find me."

River nodded, "Well you haven't yet, but you will." Brianne just smiled at River's response.

"You know you are a very frustrating person River Song." Amy countered.

Standing up Brianne chimed in, "Well I am glad I am not the only one that finds her comments frustrating."

River spoke up, "May I introduce to you; Brianne the Doctor's current companion; Brianne meet the most important Amelia Pond."

Stepping forward Brianne held out her hand, "I am so happy to finally meet you."

Amy looked over the young women and found her very familiar, but not sure why, she clasped the extended hand, "So if I am to ask you where I am in the future, you will probably respond spoilers' right."

"Yes, I would Amelia Pond so maybe it is best not to ask too many questions." Clapping her hands together she gestured to the computer screen on the fall wall. Pressing a few buttons the schematic of Area 51 was displayed on the large screen.

River whistled, "That is a lot of space to cover, have you been able to narrow it down a bit."

"Yes a bit," Brianne replied then continued as she pointed to the different rooms within the compound, "I surmised that whoever took the Doctor, knows him well so I narrowed it to places that he would have difficulties escaping from. But in there are a lot of them to check."

Amy spoke up, "So we need to get in there and search the rooms and get the Doctor out."

"Well that is what you and River are going to do." Brianne replied.

"So what are you going to do?"

"I am going to try to stay out of trouble and destroy the TARDIS prototype."

River looked at her watch, "It is going to be nightfall soon we better get ready."

Turning on the balls of her feet Brianne started to move the knobs and switches on the console, "I am going to bring the TARDIS a bit closer. We don't know what type of condition my…the Doctor is going to be in when we find him."

Moving to the other side of the controls, Brianne did a mental slap she almost gave away some important information to Amy. She was glad that it would be River accompanying Amy, as they rescued the Doctor, she was not sure if she could do it and not give away bits of Amy's future. Moving the activation switch the ship dematerialized.

Amy watched as Brianne moved along the console as she prepared the TARDIS to leave and found that the young woman moved very much like the Doctor when he flew the TARDIS.

Leaning closer to River, Amy stated, "She is more than just a companion of the Doctor's isn't she, just like you. Is she yours and the Doctor's daughter?"

River looked at Amy surprised once again at the women's intuition, "You are good, but like I said before things are never that simple when it comes to the Doctor."

"Oh, I know that, my life hasn't been simple since he walked into it." She watched as Brianne moved the activation switch then continued, "You know I never thought the Doctor could have kids but if you two ever had one I think she would be just like her. But I got to know; where did the red hair come from?"

Ignoring the question, River called out, "Don't forget the stabilizers Brianne."

"I know, I know after that time on Fieona 7 I will never forget the stabilizers again." A ringing of a bell signaled their arrival, "Okay ladies let us go and save the Doctor."

Dancing around the console Brianne moved down to one of the alcoves along the perimeter of the main room. Disappearing she returned a few moments later wearing a bronze leather coat.

River shook her head, "We are suppose to be inconspicuous."

"You guys need to be inconspicuous. I plan on walking in through the front door and saying hello." Brianne responded as she walked to the doors.

Amy confused looked at Brianne, "I don't understand, explain."

"I am going to walk through the front doors and keep our wonderful friends in there busy, while you and River find the Doctor. We don't want you to be noticed at all so I am the distraction."

"Isn't that a bit dangerous for you I wouldn't want anything to happen to you." Amy asked.

River spoke up, "Don't worry Amy, Brianne still has a very long time to live."

"What is that suppose to mean?" Amy asked frustrated.

Walking up to Amy, Brianne smiled, "It means that there is nothing to worry about, I will be fine."

Amy looked into the eyes of the young woman she reminded of the Doctor's eyes. There was no question that this was the Doctor's daughter no wonder, her Doctor needed to remain where he was.

"So come on we have things to." Brianne stated when a chime from the TARDIS rung out, "Oh yeah I almost forgot."

Amy watched as Brianne pressed another button on the console and a sonic screwdriver popped up, "Thanks my dear friend." She said as she patted the ancient machine.

Leaning toward River Amy whispered, "She is so much like him it is scary."

Chuckling River replied, "Yes, she is."

Walking out of the TARDIS the three women stepped out into the darkness.

Moving silently in the shadows they arrived at the gated perimeter of Area 51. Brianne removed the sonic screwdriver from her pocket and shined the purple light on the control panel causing the lock to release.

As they moved in Amy whispered, "Love the purple by the way."

"Thanks, it is my favorite color." Brianne replied.

"Mine too." Amy stated.

Looking at the young woman Brianne smiled sadly, "Yeah, I know."

Wondering why there was such a sad look on Brianne face, she was about to ask when they started dodging the search lights. The three of them made their way to the back entrance; using the sonic again they let themselves inside with a sigh of relief.

River pulled out her hand computer and typed a few keys, "I am getting a double heart beat, to the right that is where we should go.

"If you are getting a double heart beat then it should be easy to find the Doctor in this labyrinth. So why do you need me?" Amy asked.

"I don't know Amy, but there is a reason you left us that message and told us to bring you, so here you are." River responded.

Brianne interrupted as she started to move away, "I will head toward the left and give you the distraction that you need; look for my signal then run to the TARDIS."

"What will the signal be?" River inquired.

"You won't miss it." Brianne smiled mimicking the Doctor's words as she ran off.

"Cheeky girl." River said as she walked the opposite direction following the duel blinking lights on her computer.

Amy laughed as she followed River tiredly, contemplating what she has seen. The TARDIS didn't look any different than the one she traveled in. The relationship between River and Brianne was respectful but she doubted that River was her mother. Which made her wonder who Brianne's mum was was.

Turning a corner River stopped abruptly and kneeled close to the floor, Amy taking the cue, listen intently hearing a man's voice.

"Yeah the man in cell 13 is creepy. He never says a word he just stares out the window mumbling to hisself."

River and Amy just looked at each other knowingly as the other man replied, "I know; how much longer is going to be here?"

"Not sure." The first guard stated.

As the voices faded Amy and River moved toward cell number 13 glad that their search for the Doctor was simplified.

Brianne walked down the hall, as the Doctor always taught her, 'like she owned the place' she would flash a bit of psyche paper if needed, but so far no one question her.

As she turned a corner she heard a voice within a open room, "How is the machine responding to the calibrations? "

A female voiced answered, "Not well, I think we will need another session with the Doctor, General Nagan."

"Not going to happened, Lucille, the Doctor is slated to be silenced this afternoon. So whatever information you have will have to do."

Brianne leaned closer to hear more when someone touched her shoulder, "Please show me your credentials, ma'm."

Holding up the psyche paper she answered, "I am here from Torchwood 8 western division I was notified to come and see the prototype."

Hearing the commotion outside General Nagan came out the door, "There is no Torchwood 8 western division, at arms soldiers."

Holding her hands up, as the weapons were pointed at her Brianne stated, "Damn, I really should become more aware of the Torchwood divisions or maybe UNIT divisions so I can lie a bit better, oh well. Take me to your leader."

"Who are you ma'm?" the General asked.

"Oh I really don't want to tell you that it can cause all sorts of problems, so let's I am someone who is going to make your day a bit worse." Brianne replied with assurance.

"Take her to the interrogation room." The General ordered as he pressed an alarm on the wall, "Then go and make sure things are okay in the cell blocks, I have a feeling she isn't working alone."

"Yes sir." The soldiers replied.

River and Amy arrived at cell 13; using the hand held computer, River placed it against the key box and watched as the numbers fluctuated on the screen.

With a click the door opened, Amy rushed inside and saw a shadowed figure in the corner, moving closer she noticed the familiar outline of the Doctor, kneeling down she shook his shoulder causing the Time Lord's head to jerk upwards.

"You should not be here Amelia Pond." Then he reached for her and hugged her tightly, "But I am so glad to see you, I have missed you so very much."

Returning his hug Amy smiled into his shoulder, "I am glad to see you to, but I am sure you see Rory and me often in the future."

Looking at her sadly the Doctor replied, "Yes, I sometimes visit the town where you are at."

River hissed, "Come on Doctor, Amy we got to get going."

Standing up Amy offered her hand to the Doctor, in which he grabbed tightly loving feeling it once again. "Come on your daughter is setting up a diversion for us."

"Who told you that she was my daughter?" He inquired suspiciously.

"Oh come on Doctor, she is so much like you it is obvious. But what has me confused is that you, well the other you told me you couldn't have children." She stated as she put his arm around her shoulder to give him some support, "God, Doctor when was the last time you ate something you are all boney and your whiskers are itchy."

Chuckling weakly he smiled, "I really don't remember, but it has been a hell of a long time and I like my whiskers they make me look wise."

Shaking her head Amy replied, "No Doctor, they don't make you look wise they make you look old."

"I am 908 years old so maybe I will keep them for a while so I can look distinguished."

River stuck her head out of the cell, to check and see if the coast was clear, "Come on you two we need to start moving."

"But River where is Brianne distraction?" As Amy finished the alarm went off.

River smiled at them, "Answer and you shall receive."


	3. Chapter 3

Title: A Message in Time 3/4

Author: Flydye8

Pairings: Eleven/Amy, River/Amy, and another companion

Rating: PG-13

Disclaimer: I don't own Doctor Who I never will (sighs in sadness)

Summary: To save the Doctor from Area 51, River enlists Amy's help to save him but it may come at a cost, for the timelines are in flux all around them.

Author's Note: I have been keeping an eye on all the possible spoilers for Season 6 of Doctor Who. I have read and listen to the possible storylines. As I read and listened a plot bunny appeared to me via my muses and has demanded I write this story. I even tried to continue on my Silence series but this bunny was relentless. So here it is, maybe once I get it out of my system I can focus writing other stuff.

Brianne paid close attention to where they were going when she passed a room that had a sign on it that stated 'Top Secret', smiling to herself she moved her hand into her pocket and fiddled with her sonic screwdriver to get the right setting.

As she began to speak she settled her finger on the activation switch, "You know boys there is something I should tell you."

"Silence you we don't care what you have to say." One of the soldiers replied.

"You really should listen to what I am saying because it could save you from a lot of pain."

"Shut up prisoner."

"I tried to warn you but since the lot of you, are stubborn I guess you will feel the pain." Brianne pressed the activation switch which caused the sonic to emit a high pitch sound; the soldiers fell to the ground holding their ears in pain.

"I tried to warn you, maybe next time you will listen." Brianne ran to the door that she saw earlier and sonic it opened. As she moved inside she jammed the lock with another frequency. Turning away from the door she sighed in relief that no one else was in the room.

Looking around she said out loud, "I guess they are always bigger on the inside."

Walking up to the TARDIS prototype she examined the circuitry, and found that the developers were dangerously close to completing it. She moved her fingers along the console, then yanked her hand back as the lights started to blink. Hearing a dull hum in the back of her head she knew immediately that the machine was sentient.

An image of a man with long dark hair, which Brianne didn't recognize appeared, "Response message Alpha, Omega activated. Brianne, it is about time you got here."

Shocked that the image knew her name, she waited for it to continue, "I know that you are going to destroy this TARDIS but it is imperative that you don't. It has been grown from the TARDIS you traveled in and it needs a pilot. You are young enough to connect with this infant TARDIS so that it won't be overloaded. I have taught you enough that you can fly her safely from this facility."

The image looked at his watch then continued, "It is time for you to leave with this TARDIS which I am sure will be associated with a big bang. Tell me to bring this TARDIS some place safe and let it grow naturally without outside influence, I will see you soon my daughter."

Brianne watched as the image faded now knowing who was in the image, the fact that it was a future incarnation of her father sent a shiver down her spine. Shaking off the feeling of apprehension, she placed her hands on one of the ovals. Immediately she felt hum turn into words in her mind as the TARDIS spoke to her, "_Welcome little one_."

Smiling Brianne replied silently, _"Thank you. Now what am I suppose to do?"_

"_Fly me out of here and make sure the people here don't cause problems again"_

"_I have to get the humans out of here first and set this facility back about twenty years." Brianne replied._

"_Do what you must but hurry." The infant TARDIS responded._

Running to the door Brianne un-jammed the door lock and peeked in each direction of the hallway. Seeing that no one was around she moved to the right looking for a room that can give her the big bang that her father's recording referred to.

Looking at the signs associated with the doors, she paused as a large smile graced her features, "Ahh yes, this will do nicely."

Amy and River held the Doctor up in-between them as they moved along the shadows, when they heard soldiers moving in their direction they ducked into a small room out of sight.

Once in the room the Doctor collapsed on the floor breathing a bit more heavily, Amy asked worriedly, "Are you alright, you usually are not as winded as you are now."

Catching his breath he replied sarcastically, "I have been stuck in a small cell for three months, barely anything to eat, with a mattress I swear was stuffed with rocks for a bed. Yes, I am a bit weak."

"But not too weak to speak I see." Amy responded chuckling.

River knelt down and did a full body scan on the Doctor, "I should have done this before we started moving." Looking at the read out she reported, "Well nothing out of the ordinary is wrong with you. I would say fatigue is your major complication."

"I just said that." Looking at Amy he asked, "Didn't I just say that?"

River continued as if the Doctor didn't interrupt, "But your energy reserves are dangerously low, we can't keep moving at this pace otherwise you are going to pass out on us, then we will really have problems moving you."

"I do not pass out, River, I go into a restorative sleep for a long period of time." The Doctor stated.

Amy looked at River, "So he passes out then."

"Yes, he passes out."

"So what should we do?" The young red head inquired.

Looking at her map River replied, "Down the passageway and to the right is open alcove used to venting air in and out of the facility. If we can get there you two can hide in there as I retrieve the TARDIS and bring her to you."

"Sounds like a plan, lead the way." Looking down at the Doctor Amy noticed that his eyes had closed. Giving him a gentle slap on the cheek she spoke persistently, "Oi, Doctor no sleeping on the job. Come on let's get moving the sooner we are out of her the better."

Opening his eyes he smiled, "Your voice is so sexy when you speak that way."

"Can fatigue cause delusions in Time Lords." Amy asked River as they hefted him between them again.

"Not sure, I have never seen him this weak before." The older woman replied as they started to move toward the air venting shaft.

Brianne used her sonic to enter the room that was labeled 'Broiler room' immediately the heat of the space caused beads of sweat to emerge on her brow. Walking to the main console she adjusted the temperature gauge, so that the water inside the huge metal spheres would reach critical limits in about ten minutes. Disengaging the safety protocols she watched as the gauges started to rise, signaling the increase of steam pressure.

Deciding that the explosion would be enough to cripple the facility she left the room as the alarms and Claxton bells began to sound. Emerging in the hall she moved quickly back to the area that held the infant TARDIS.

Walking up to the main console of the time machine she placed her hands on the circles, "Okay let us get out of here." A confirmatory hum sounded inside her mind as Brianne typed in the rendezvous coordinates, that she and River agreed upon, before starting the dematerialization sequence.

Moving in a circle Brianne pushed the each switch activating the time matrix. As she pushed the last one, she watched, as beams of light projected into the center from the switches, converging into a single beam that moved upwards and then down through the circuitry of the walls.

Brianne smiled as the familiar sound of the rotor moving echoed through the chamber, pressing the buttons that the TARDIS illuminated on the console, the ship disappeared from the space as the countdown for the broiler explosion reached two minutes.

Arriving at the venting shaft the Doctor collapsed into Amy's arms. With River's assistance they laid him on the floor.

Pushing the hair from his forehead Amy asked, "Is he going to be alright?"

Scanning him once again River responded, "Yeah, he is in his restorative sleep mode. He should be okay in a few hours."

Sighing with relief Amy cradled his head in her lap running her hands through his hair, "You know I have only seen him sleep once. Before that night, I thought he never slept and I haven't seen him sleep since."

River smiled knowingly, "I am going to get the TARDIS I will be back here very soon."

"What should I do till you return?"

"Hold him, Amy and let him know you are here with him. He has missed you terribly."

"And how do you know that…never mind spoiler's right." Amy responded.

"Yes Amy, spoilers, I will be back soon."

River moved quickly and stealthily through the red lighted halls, reaching the door that lead to the outside she opened it and used the shadows for cover. When she was about halfway to the gate she heard the alarm bells go off causing the personnel of the compound to rush around. As two soldiers approached her she ducked behind one of the parked vehicles.

Listening intently she heard one soldier speak to another, "Report private." The older man stated.

"Sir, someone has sabotaged the broilers, the pressure within in them will cause them to explode in about two minutes we have been given the order to evacuate."

"Well hurry than private get as many personnel out of the compound and meet at the rendezvous coordinates."

"Yes sir!" The private stated as he obeyed his superiors command.

As River heard the footsteps fade she moved from her hiding place smiling, 'good ole Brianne'. Quickly exiting the ground she ran to the TARDIS she didn't have much time to get the Doctor and Amy out.

Reaching the outcropping of red rocks Brianne asked the TARDIS

"_Is the chameleon circuit active?"_

"_Confirmed." _

"_Then let us land over there near the rocks"_

"_Agreed." The TARDIS replied._

Once the dematerialization of the new machine was complete a door appeared to Brianne's right. Moving toward it she opened it to find herself facing the desert. Stepping out she looked behind her and found that the TARDIS's exterior looked just like the rocks surrounding it.

"Very cool." She simply stated as she grabbed the binoculars from her jacket to watch the activity around area 51. She hoped that River and Amy were able to get her father out as she mentally counted down the time to the explosion.

Amy sat with the Doctor as the alarms bells rang out within the compound, pulling him closer to her chest she whispered, "Don't worry Doctor, I got you. I will keep you safe."

Almost immediately Amy felt the ground shake underneath her causing the walls along the shaft to start to crack. She watched horrified as the cracks continued toward the large air blades above her. Once there the cracks stopped, and Amy breathed a sigh of relief.

Her relief was short lived though as another explosion shook the foundation causing the large blades to be jostled and loosen the bolts holding them in place. Amy closed her eyes and spoke softly, "Please hurry River, Please hurry!"


	4. Chapter 4

**Thank you for reading I do hope you enjoyed my little take of season 6 Flydye**

Title: A Message in Time 4/4

Author: Flydye8

Pairings: Eleven/Amy, River/Amy, and another companion

Rating: PG-13

Disclaimer: I don't own Doctor Who I never will (sighs in sadness)

Summary: To save the Doctor from Area 51, River enlists Amy's help to save him but it may come at a cost, for the timelines are in flux all around them.

Author's Note: I have been keeping an eye on all the possible spoilers for Season 6 of Doctor Who. I have read and listen to the possible storylines. As I read and listened a plot bunny appeared to me via my muses and has demanded I write this story. So without any more delay here is the conclusion of "A Message in Time"

River ran toward the TARDIS as an explosion erupted behind her, momentarily knocking her to the ground. Picking herself up quickly, she sprinted the last few feet to the blue wooden doors, closing the doors behind her another explosion rocked the area. Running up to the center console River quickly moved the TARDIS to where the Doctor and Amy were waiting for her.

In the air shaft Amy eyed the fans wearily as two more bolts were severed by the weight of the blades, which were now pointing downwards, held by one final bolt. Amy looked around frantically for anything she could use shield them, but nothing around them could keep them safe from harm.

Getting up on her feet she tried to drag the Doctor closer to the wall but after moving him only inches she knew she would not be able to move him much further. Gathering the Doctor in her arms she held him tightly, kissed his forehead and whispered, "No, matter what happens, I will always love you my raggedy old Doctor."

Hearing the last bolt break Amy leaned over the Doctor, preparing herself for the impact of the blade when the familiar sound of the TARDIS echoed in the enclosed space. As the outer shell of the TARDIS surrounded them a loud clang rung out, as the blade impacted with the top of the police box.

Amy breathed a sigh of relief then chastised, "Why is it that you and the Doctor always wait till the last minute to save the day?"

River just chuckled, "Because it is more fun that way sweetie.

Brianne paced the ground apprehensively waiting for the other TARDIS to materialize, checking her watch for the seemed to be the millionth time, she was about to go look for River and the others when the wind around her picked up and the sound of her father's TARDIS echoed around her.

She breathed a sigh of relief as the familiar blue box appeared in front of her, soon after River poked her head out the doors, "Come on Brianne we need your help moving the Doctor."

Seeing her father on the floor next to Amy, Brianne rushed to his side, "Oh dad what have they done to you?"

Amy looked at the young women and answered sympathetically, "He will be okay Brianne, they didn't do anything, except cause him a lot of fatigue. But according to River we need to get him to the med-bay just to be sure."

Kneeling at the Doctor's feet, River ordered, "I will grab his feet as each of you grabs an arm."

Between the three of them, they somehow moved the Doctor into the med bay and onto the examining bed. River immediately set up the instruments to scan the Doctor as he slept, turning toward the others she stated, "The TARDIS will let us know if anything changes. I don't know about you, but I could use a good cup of coffee."

"Nope I think I will pass, I want to stay here with the Doctor." Amy stated as she grabbed the Doctor's hand and sat by his side."

"Very well, what about you Brianne?" River inquired.

Not trusting herself to be in the same room as Amy, Brianne replied, "Yes, I think I will join you the Doctor is in good hands."

Amy watched as the two women exited the med bay then brought her attention back to the Doctor, "Sleep well my Time Lord I will be here when you wake up."

Brianne and River sat at the kitchen table sharing stories about what happened to each of them after they separated at Area 51.

Brianne sat back in her chair as she finished and asked, "So when do you think my father will regenerate into the person I saw in the recording?"

"You know I can't tell you that sweetie, but I will tell you that the man you saw is the one that I traveled with."

"You know I don't think I will ever get use to this timey-whimey stuff."

Reaching across the table, River took Brianne's hand, "You will understand the timey-whimey stuff eventually I promise."

Brianne tilted her head to the side as the TARDIS hummed persistently in her mind, "Dad is waking up we better head back to the med bay."

Amy was not sure when she fell asleep on the Doctor's chest but as his body moved under her she lifted her head and found him staring at her fondly, "Hello Amelia Pond."

"Hello Doctor, I am glad to see you awake. How are you feeling?"

"Much better thanks to some restorative sleep."

"Good but you still look like an old man with all those whiskers." Amy teased.

Reaching up he stroked his facial hair, "Didn't you know Pond that whiskers are cool."

Laughing she hugged him tightly; "You have no idea how glad I am to hear you say that."

"Were you worried about me Amy?" he said as he touched her hair.

Pulling back from him she replied, "Yeah I was worried about you, my Doctor"

"Well there was no need to worry, Time Lord's are hard to keep down, but you know what I want right now."

"What is that Doctor?"

"I want a shower and a good cup of tea."

"If that is what you want, then that is what you get. Come on let me help you to the loo so you can get cleaned up."

Placing his arm around her shoulder she was about to lift him when he stopped her, "Amy what year did River and Brianne pick you up from?"

"Why do you need to know?"

"Please Amy, tell me what year."

"Well the year for me is 2011, I think it is around September but I am not sure. You know how it is it can be a bit confusing traveling about the universes."

The Doctor pulled away from Amy, "You should not be helping me up it is not safe for you or our…"

River interrupted as she walked into the room with Brianne close behind, "Doctor, spoilers." Moving to his side River helped him out of the bed and into the bathroom, "Let me help you get cleaned up then we can bring Amy back to her TARDIS before Rory and the other you wake up."

The Doctor nodded as he allowed River to assist him, leaving Brianne with Amy.

Amy looked at the other young women and asked with a broken sob, "What the hell is going on? What are you guys not telling me?"

Brianne stepped closer to Amy and grabbed her hands and touched Amy's forehead with hers, "Listen, I know that not knowing is hard, but if we are not careful what is meant to happen won't"

As the tears fell down her cheeks Amy gasped, "But time can be re-written."

Brianne choked back her own tears, "Yes, it can but the timeline you are in right now needs to stay the same…my existence depends on it."

Pulling away Amy looked into Brianne's eyes, "Why does your existence depend on it."

"I have already said to much, come on let us get you some tea and wait for the Doctor to finish. Then we will get you home."

The Doctor and River walked into the kitchen area as Amy and Brianne were finishing their tea.

Amy looked at the Doctor and gave her nod of approval, "Now that is the Doctor that I know, you still look a bit older but I guess that is to be expected since you are from the future."

He looked at her sadly, "Well some things age a man a bit more than others."

River looked at her watch, "We really need to get you back Amy otherwise your Doctor is going to come searching for you."

Standing up Amy put her cup in the sink, "Yeah I think it is time to get back, all the secrets you guys are keeping from me is very frustrating."

Grabbing Amy's hand the Doctor led her through the ship and into the brisk night air. Once outside the ship the Doctor moved her away from the others and embraced her firmly, "I am going to miss you Amelia Pond."

"I wouldn't say that Doctor, you are about to see me."

Laughing he stated, "Well you are right on that point." Then as he placed his forehead against hers he continued soberly, "I want you to promise me something."

"Sure, anything." Amy replied.

"Promise me that whatever happens in the next few months that you will be honest with me about everything."

"I am always honest with you Doctor."

"I am serious Amelia, promise me." He insisted.

"Okay, okay I promise."

"Good, Good, thank you for your promise." Leaning down he kissed her lips, "And never forget that I will always love you."

Pulling away from him she smiled, "And the same goes for me, my raggedy Doctor."

Brianne stepped forward and embraced Amy, "I will see you again very soon, but till then stay safe and well."

"I will." Amy replied with a smile.

"Come on Amy we need to get you home." River stated then turned toward the Doctor, "And I will see you again soon."

"I am looking forward to it River." The Doctor replied.

"Oh Doctor, you never look forward to seeing me." River replied with her hands on her hips, "But thank you for saying you will."

The Doctor grabbed Brianne's hand as they watched Amy and River walk away, "How are you doing my daughter."

With tears in her eyes Brianne replied, "Oh Dad, considering that I just met my mum who died while giving birth to me, I am doing okay. How are you doing it must have been hard to see her?"

"It is hard to see her again, but I think I am doing okay as well." Turning toward his daughter he continued, "So where should we go next Brianne Amelia Pond."

Pulling her Dad toward the infant TARDIS, Brianne smiled, "I think we need to go somewhere so that my TARDIS can finish growing. Wait till you see her, she is gorgeous, and you know what is even better, her chameleon circuit is working."

"Well of course it is working; I was the one that gave them the specs on how to build it."

"Well if you know how to fix it why don't you fix the chameleon circuit on your ship?"

Smiling down at her he replied, "Because police boxes are cool."

The Doctor woke up around the same time Rory did, moving to the console he scanned the surrounding area for Amy.

In the middle of his search Amy walked in, "Hello, my boys I am home."

Hurrying down the steps the Doctor embraced his companion, "Are you okay did that vile woman hurt you."

"Doctor I am fine, just a bit tired."

"Why are you tired Amy." Rory asked as he embraced his wife.

Amy just smiled, "Spoilers."

A few weeks later Amy looked at the stick in her hand and read the results, smiling she clapped her hands together and went in search of the Doctor so that he could confirm the results.

She found him under the console of his TARDIS, pulling him out Amy stated, "I need your help."

"What do you need my help with?"

"Come on we need to go to the med bay." dragging him by the arm down the passageway.

Once in the sterile looking room the Doctor asked, "So what is this all about Pond?"

Pulling put the pregnancy test out she replied, "This says I am pregnant and with all this high tech medical equipment I thought you could confirm it for me before I tell Rory."

Smiling happily the Doctor clapped his hands, "Well lay down on the bed and we will take a look of this bundle of joy."

Turning on the ultrasound equipment the Doctor put some blue gel on Amy's stomach, and placed the readout arm on her tummy. Moving a bit back and forth across her tummy, the Doctor found the heartbeat of the baby turning up the volume with a smile.

Soon the sound of the baby's heart echoed in the room, moving the arm slightly to the left the heartbeat changed and the smile on the Doctor's face changed to disbelief.

Seeing the change Amy asked, "What is it Doctor? Is the baby okay?"

Removing the arm from Amy's tummy the Doctor stated somberly, "Yes the baby is perfectly fine for a Gallifreyan."

"What do you mean for a Gallifreyan?" Amy asked.

Sitting on the bed next to her the Doctor explained, "I am so sorry, the baby you are carrying is not Rory's it is mine."

Sitting up Amy caressed the Doctor's face, "Why are you sorry I am not. The night we spent together was magical and look," Pointing to the image on the ultrasound machine, "We created a beautiful life."

"Oh Amy don't you see; I have ruined any chance of happiness for you."

"Do you regret making love to me?" Amy asked apprehensively.

Cupping her face with his hands placing his forehead against the Doctor whispered, "Never, Amelia, never you are right it was magical."

Amy smiled now understanding why Brianne, River, and the other Doctor were so secretive, "Our daughter is going to be beautiful, smart and brilliant just like just like her father and I couldn't be happier."

"How do you know it will be a girl?"

"Because, I have met her and she is all the things I have mentioned and more." Amy stated proudly.

"You have met her. How? Wait is she ginger like you?"

"I met her when at Area 51 and yes, she is ginger like me but she is very much like her father." Amy stated.

Sighing the Doctor asked, "What are we going to do? How are we going to tell Rory?"

Feeling a bit apprehensive at the thought of telling Rory, Amy shook it off as she leaned toward the Doctor, kissing him before responding, "I don't know but we will manage somehow, my Doctor."

Returning her kiss the Doctor smiled on her lips, "You know, this changes everything and it will be difficult."

"Yes, it does but I think it will be a good change."

"Yes, very good, very good indeed." The Doctor replied as he kissed Amy's lips once again.


End file.
